OBO::CCO::OrthoMCLParser - An orthoMCL data to OBO translator
Includes methods for adding information from orthoMCL data files to ontologies
orthoMCL can be obtained from http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi
The method 'parse()' parses an orthoMCL output data file into a data structure (hash of arrays) The method 'work()' incorporates data from an orthoMCL data file into an ontology, writes the ontology into an OBO file, writes map files.
Vladimir Mironov vlmir@psb.ugent.be
Copyright (C) 2006 by Vladimir Mironov
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.
Usage - $OrthoMCLParser->parse() Returns - A a reference to a data structure (hash of hases) containing orthoMCL output data Args - orthoMCL output data file Function - parses an orthoMCL output data file into a data structure
Usage - $OrthoMCLParser->work($omcl_data_ref, $file_names_ref, $taxa_ref) Returns - OBO::Core::Ontology object Args - 1. reference to an orthoMCL data structure (output of parse()), 2. reference to a list of filenames (output OBO file, 4 map files (U,T,O,B, see the test file), 3. reference to a with taxons and taxon specific maps (see the test file) Function - converts orthoMCL data into an ontology, writes OBO and map files
To install OBO::Core::Def, copy and paste the appropriate command in to your terminal.
cpanm
cpanm OBO::Core::Def
CPAN shell
perl -MCPAN -e shell install OBO::Core::Def
For more information on module installation, please visit the detailed CPAN module installation guide.